sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4o95 | 245 | Cytokinin dehydrogenase 4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4o95 | 245 | Cytokinin dehydrogenase 4 | / | 1.000 | |
| 4oal | 245 | Cytokinin dehydrogenase 4 | / | 0.612 | |
| 1w1r | ZEA | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.567 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.552 | |
| 3s1c | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.538 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.508 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.503 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.502 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.500 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.486 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.483 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.481 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.481 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.480 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.478 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.478 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.474 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.474 | |
| 3ibe | L64 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.472 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.470 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.470 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.470 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.468 | |
| 4ezl | 0SE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.468 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.468 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.468 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 2i0y | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.467 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.466 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.466 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.466 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.466 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.465 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.464 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.463 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.463 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.462 | |
| 3cse | N22 | Uncharacterized protein | / | 0.462 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.462 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.461 | |
| 2pul | ACP | Methylthioribose kinase | 2.7.1.100 | 0.461 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.461 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 3eem | 53V | Uncharacterized protein | / | 0.460 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.459 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3bej | MUF | Bile acid receptor | / | 0.459 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.459 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 3gc8 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.458 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.458 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.458 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 4otp | ADP | Serine/threonine-protein kinase RIO1 | 2.7.11.1 | 0.457 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.457 | |
| 1d2s | DHT | Sex hormone-binding globulin | / | 0.456 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.456 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.456 | |
| 2dr3 | ADP | UPF0273 protein PH0284 | / | 0.455 | |
| 2pml | ANP | Uncharacterized protein | / | 0.455 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.455 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 4iv2 | 1GR | Estrogen receptor | / | 0.455 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.455 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 4c61 | LMM | Tyrosine-protein kinase JAK2 | / | 0.453 | |
| 4dph | P65 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.452 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.452 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.452 | |
| 3kk6 | CEL | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.452 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.452 | |
| 4z9r | NAD | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.452 | |
| 2e9n | 76A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.451 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.451 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.451 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 4bbf | O19 | Tyrosine-protein kinase JAK2 | / | 0.450 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.450 | |
| 4m15 | ADP | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.450 | |
| 1syn | F89 | Thymidylate synthase | / | 0.449 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.449 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.449 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4dca | ADP | Aminoglycoside phosphotransferase | / | 0.449 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.449 | |
| 4xwt | U5P | Ribonuclease J | / | 0.449 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.448 | |
| 3q0u | LL3 | HTH-type transcriptional regulator EthR | / | 0.448 | |
| 3qts | X46 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.448 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3cr7 | PPS | Adenylyl-sulfate kinase | 2.7.1.25 | 0.447 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.446 | |
| 1ie4 | T44 | Transthyretin | / | 0.446 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
| 4a2z | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4bbh | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.445 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.445 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.445 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.445 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4i2p | G73 | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.445 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1fml | RTL | Retinol dehydratase | / | 0.444 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.444 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2bro | DF2 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.444 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3zux | TCH | Transporter | / | 0.444 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.443 | |
| 3lu8 | IQX | Serum albumin | / | 0.443 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.443 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.443 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.443 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 1v1k | 3FP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.442 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1hqu | HBY | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1oi9 | N20 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.441 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.441 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3mde | CO8 | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2zpa | ADP | tRNA(Met) cytidine acetyltransferase TmcA | / | 0.440 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 | |
| 3bgr | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.440 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.440 | |
| 3x0c | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.440 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.440 | |
| 5a28 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |